Aran is a fourth year medical student at James Cook University in Townsville. He graduated from Trinity Grammar School in Sydney, but was born in Singapore and lived in London. During his spare time he enjoys running and playing chess online.
Aran’s project is predicting protein-protein interaction motifs in KLF transcription factors.
This got a bit buried in all the conference excitement but congratulations to our lab neighbours and journal club buddies for winning the Research Category at the inaugural #BABSFEST video competition:
Early bird deadline is 1st November 2015 so register now for $$$ savings.
The Australian Bioinformatics And Computational Biology Society (ABACBS) 2015 Conference is almost upon us and the lab has four posters. Come visit us if you are attending! If not, you can check them out on the Australian Bioinformatics And Computational Biology Society Conference F1000Research channel and tweet or email with questions:
FF5. The SMRT Way to Sequence a Yeast Genome. Åsa Pérez-Bercoff, Tonia L. Russell, Paul V. Attfield, Philip J.L. Bell & Richard J. Edwards. http://f1000research.com/posters/4-1022.
FF6. Evidence for viral causes of cancer in prostate cancer transcriptomes and genomes. Timothy G. Amos, James S. Lawson, Wendy K. Glenn, Noel J. Whitaker & Richard J. Edwards. http://f1000research.com/posters/4-1023.
P20. SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. Emily Olorin, Kevin T. O’Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields & Richard J. Edwards. http://f1000research.com/posters/4-1024.
P27. Genetic Characterisation of the Evolution of a Novel Metabolic Function in Yeast. Åsa Pérez-Bercoff, Tonia L. Russell, Paul V. Attfield, Philip J.L. Bell & Richard J. Edwards. http://f1000research.com/posters/4-1025.
Åsa Pérez-Bercoff, Tonia L. Russell, Paul V. Attfield, Philip J.L. Bell & Richard J. Edwards. http://f1000research.com/posters/4-1025.
We have a unique opportunity to study how new biological pathways have evolved to produce a yeast with a novel metabolic activity. Thirty-seven Saccharomyces cerevisiae strains were grown as a mixed population, and adapted on a specific media for 1463 days, undergoing sexual mating every two months. As a pilot study, three of the ancestral strains from the starting population, including two diploids, were selected for new PacBio RSII long-read single molecule real time (SMRT) sequencing at the Ramaciotti Centre for Genomics. High quality complete genomes were assembled de novo using the hierarchical genome-assembly process (HGAP3) using only PacBio non-hybrid long-read SMRT sequencing data, and corrected using Quiver. In addition, we have shotgun metagenomic Illumina data from a population exhibiting early adaptation to growth on the selective media. We are developing methods to map these short-read data onto several high quality ancestral genomes in order to estimate the relative contribution of each ancestor’s genetic variation to the evolved population, and identify possible sites of recombination. In addition, metagenomic data is being mapped against the official S. cerevisiae reference strain S288c to conduct variant calling to identify single nucleotide polymorphisms (SNPs) that are not present in any of our ancestral or reference genomes. These will be compared to the publicly available “100 yeast genomes”, and partitioned into natural variation and candidates for novel mutations. By doing these comparisons we hope to elucidate how the population has evolved to acquire its novel characteristics.
